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Hi @haghshenas , I am so sorry to borror you,but I meet a problem when I run ../runCorr.sh pac.fasta ill.fastq testCorr pre 4.

the run result as follows:
[bwa_index] Pack FASTA... 0.01 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.16 seconds elapse.
[bwa_index] Update BWT... 0.03 sec
[bwa_index] Pack forward-only FASTA... 0.01 sec
[bwa_index] Construct SA from BWT and Occ... 0.08 sec
[main] Version: 0.7.10-r960-dirty
[main] CMD: ../bin/bwa-proovread index /itmslhppc/itmsl01_02/colormap/testData/testCorr/pre_uncorr.fasta
[main] Real time: 0.298 sec; CPU: 0.296 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::main_mem] read 24250 sequences (2425000 bp)...
[M::mem_process_seqs] Processed 24250 reads in 26.452 CPU sec, 6.631 real sec
[main] Version: 0.7.10-r960-dirty
[main] CMD: ../bin/bwa-proovread mem -aY -A 5 -B 11 -O 2,1 -E 4,3 -k 8 -W 16 -w 40 -r 1 -D 0 -y 20 -L 30,30 -T 2.5 -t 4 /itmslhppc/itmsl01_02/colormap/testData/testCorr/pre_uncorr.fasta /itmslhppc/itmsl01_02/colormap/testData/ill.fastq
[main] Real time: 6.719 sec; CPU: 26.537 sec
*** Error in `../bin/spCorrection': free(): invalid pointer: 0x00002b77e005a2c0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x2b77dba40299]
../bin/spCorrection[0x40fe4a]
../bin/spCorrection[0x40444c]
/lib64/libpthread.so.0(+0x7ea5)[0x2b77daf8aea5]
/lib64/libc.so.6(clone+0x6d)[0x2b77dbabd96d]
======= Memory map: ========
00400000-00403000 r--p 00000000 08:04 14010288873 /itmslhppc/itmsl01_02/colormap/bin/spCorrection
00403000-00419000 r-xp 00003000 08:04 14010288873 /itmslhppc/itmsl01_02/colormap/bin/spCorrection
00419000-00420000 r--p 00019000 08:04 14010288873 /itmslhppc/itmsl01_02/colormap/bin/spCorrection
00420000-00421000 r--p 0001f000 08:04 14010288873 /itmslhppc/itmsl01_02/colormap/bin/spCorrection
00421000-00422000 rw-p 00020000 08:04 14010288873 /itmslhppc/itmsl01_02/colormap/bin/spCorrection
00422000-00423000 rw-p 00000000 00:00 0
00432000-00557000 rw-p 00000000 00:00 0 [heap]
2b77dab49000-2b77dab6b000 r-xp 00000000 08:04 2147491372 /usr/lib64/ld-2.17.so
2b77dab6b000-2b77dab6d000 rw-p 00000000 00:00 0
2b77dab90000-2b77dac96000 rw-p 00000000 00:00 0
2b77dad6a000-2b77dad6b000 r--p 00021000 08:04 2147491372 /usr/lib64/ld-2.17.so
2b77dad6b000-2b77dad6c000 rw-p 00022000 08:04 2147491372 /usr/lib64/ld-2.17.so
2b77dad6c000-2b77dad6d000 rw-p 00000000 00:00 0
2b77dad6d000-2b77dad82000 r-xp 00000000 08:04 2147491465 /usr/lib64/libz.so.1.2.7
2b77dad82000-2b77daf81000 ---p 00015000 08:04 2147491465 /usr/lib64/libz.so.1.2.7
2b77daf81000-2b77daf82000 r--p 00014000 08:04 2147491465 /usr/lib64/libz.so.1.2.7
2b77daf82000-2b77daf83000 rw-p 00015000 08:04 2147491465 /usr/lib64/libz.so.1.2.7
2b77daf83000-2b77daf9a000 r-xp 00000000 08:04 2147491405 /usr/lib64/libpthread-2.17.so
2b77daf9a000-2b77db199000 ---p 00017000 08:04 2147491405 /usr/lib64/libpthread-2.17.so
2b77db199000-2b77db19a000 r--p 00016000 08:04 2147491405 /usr/lib64/libpthread-2.17.so
2b77db19a000-2b77db19b000 rw-p 00017000 08:04 2147491405 /usr/lib64/libpthread-2.17.so
2b77db19b000-2b77db19f000 rw-p 00000000 00:00 0
2b77db19f000-2b77db288000 r-xp 00000000 08:04 2147491419 /usr/lib64/libstdc++.so.6.0.19
2b77db288000-2b77db488000 ---p 000e9000 08:04 2147491419 /usr/lib64/libstdc++.so.6.0.19
2b77db488000-2b77db490000 r--p 000e9000 08:04 2147491419 /usr/lib64/libstdc++.so.6.0.19
2b77db490000-2b77db492000 rw-p 000f1000 08:04 2147491419 /usr/lib64/libstdc++.so.6.0.19
2b77db492000-2b77db4a7000 rw-p 00000000 00:00 0
2b77db4a7000-2b77db5a8000 r-xp 00000000 08:04 2147491387 /usr/lib64/libm-2.17.so
2b77db5a8000-2b77db7a7000 ---p 00101000 08:04 2147491387 /usr/lib64/libm-2.17.so
2b77db7a7000-2b77db7a8000 r--p 00100000 08:04 2147491387 /usr/lib64/libm-2.17.so
2b77db7a8000-2b77db7a9000 rw-p 00101000 08:04 2147491387 /usr/lib64/libm-2.17.so
2b77db7a9000-2b77db7be000 r-xp 00000000 08:04 2147484162 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b77db7be000-2b77db9bd000 ---p 00015000 08:04 2147484162 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b77db9bd000-2b77db9be000 r--p 00014000 08:04 2147484162 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b77db9be000-2b77db9bf000 rw-p 00015000 08:04 2147484162 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b77db9bf000-2b77dbb83000 r-xp 00000000 08:04 2147491379 /usr/lib64/libc-2.17.so
2b77dbb83000-2b77dbd82000 ---p 001c4000 08:04 2147491379 /usr/lib64/libc-2.17.so
2b77dbd82000-2b77dbd86000 r--p 001c3000 08:04 2147491379 /usr/lib64/libc-2.17.so
2b77dbd86000-2b77dbd88000 rw-p 001c7000 08:04 2147491379 /usr/lib64/libc-2.17.so
2b77dbd88000-2b77dbd8d000 rw-p 00000000 00:00 0
2b77dbd8d000-2b77dbd8e000 ---p 00000000 00:00 0
2b77dbd8e000-2b77dbf8e000 rw-p 00000000 00:00 0
2b77dbf8e000-2b77dbf8f000 ---p 00000000 00:00 0
2b77dbf8f000-2b77dc18f000 rw-p 00000000 00:00 0
2b77dc18f000-2b77dc190000 ---p 00000000 00:00 0
2b77dc190000-2b77dc390000 rw-p 00000000 00:00 0
2b77dc390000-2b77dc391000 ---p 00000000 00:00 0
2b77dc391000-2b77dc591000 rw-p 00000000 00:00 0
2b77e0000000-2b77e01cd000 rw-p 00000000 00:00 0
2b77e01cd000-2b77e4000000 ---p 00000000 00:00 0
2b77e8000000-2b77e826f000 rw-p 00000000 00:00 0
2b77e826f000-2b77ec000000 ---p 00000000 00:00 0
2b77f0000000-2b77f01db000 rw-p 00000000 00:00 0
2b77f01db000-2b77f4000000 ---p 00000000 00:00 0
2b77f8000000-2b77f8180000 rw-p 00000000 00:00 0
2b77f8180000-2b77fc000000 ---p 00000000 00:00 0
7ffe9fb80000-7ffe9fba1000 rw-p 00000000 00:00 0 [stack]
7ffe9fbce000-7ffe9fbd0000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
../runCorr.sh: line 38: 169304 Aborted (core dumped) ${SPALG} -l ${UNCORR}.fasta -a ${ITER1}.sort.sam -t ${NTHREAD} > ${ITER1}.fasta
[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 314: Success
[E::bwa_idx_load_from_disk] fail to locate the index files
rm: cannot remove ‘/itmslhppc/itmsl01_02/colormap/testData/testCorr/pre_iter1.fasta.amb’: No such file or directory
rm: cannot remove ‘/itmslhppc/itmsl01_02/colormap/testData/testCorr/pre_iter1.fasta.ann’: No such file or directory
rm: cannot remove ‘/itmslhppc/itmsl01_02/colormap/testData/testCorr/pre_iter1.fasta.bwt’: No such file or directory
rm: cannot remove ‘/itmslhppc/itmsl01_02/colormap/testData/testCorr/pre_iter1.fasta.sa’: No such file or directory
No sam entries in file: /itmslhppc/itmsl01_02/colormap/testData/testCorr/pre_iter2.sort.sam

I use CentOS system and look forward to your reply!
Thank you very much!

Hey,
I apologise to disturb you. At this moment, I have finished run the prepare step for short reads, then starting to long-reads error correction. However, my long reads contain 200 Gb in one compressed fastq.gz file. Can I use the compressed fastq files on long-reads correction.

best wish
erbo

Dear author, thank you for your excellent software development. I met the following problems during installation. Could you please help me to check what is the problem

git clone --recursive https://github.com/sfu-compbio/colormap.git
Cloning into 'colormap'...
remote: Enumerating objects: 80, done.
remote: Total 80 (delta 0), reused 0 (delta 0), pack-reused 80
Unpacking objects: 100% (80/80), done.
Submodule 'utils/bwa' (https://github.com/BioInf-Wuerzburg/bwa.git) registered for path 'utils/bwa'
Submodule 'utils/htslib' (https://github.com/samtools/htslib.git) registered for path 'utils/htslib'
Submodule 'utils/minia' (https://github.com/GATB/minia.git) registered for path 'utils/minia'
Submodule 'utils/samtools' (https://github.com/samtools/samtools.git) registered for path 'utils/samtools'
Submodule 'utils/utils' (https://github.com/sfu-compbio/utils.git) registered for path 'utils/utils'
Cloning into 'utils/bwa'...
error: RPC failed; result=35, HTTP code = 0
fatal: The remote end hung up unexpectedly
Clone of 'https://github.com/BioInf-Wuerzburg/bwa.git' into submodule path 'utils/bwa' failed

Since it is possible to run spCorrection more than once, it should be aware of already corrected and uncorrected regions, so that the second round of running always outputs already corrected regions as corrected again (by upper-case characters).

Hi, everyone,
the command to correct the read is : ./runCorr.sh <pacbio.fasta> <illumina.fastq>
However, it did not mention that how to deal it with multiple pacbio and illumina files?
especially, the paired-end files contained two files. is there any advices? Thanks very much!

Best wishes,
Xiaoting

Hi,
I had installed the software with readme. But when I run testData using given step and following problems appares:

../runCorr.sh pac.fasta ill.fastq testCorr pre 4

[bwa_index] Pack FASTA... 0.02 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.27 seconds elapse.
[bwa_index] Update BWT... 0.01 sec
[bwa_index] Pack forward-only FASTA... 0.01 sec
[bwa_index] Construct SA from BWT and Occ... 0.14 sec
[main] Version: 0.7.10-r960-dirty
[main] CMD: ../bin/bwa-proovread index /home/sunyangbo/software/colormap/testData/testCorr/pre_uncorr.fasta
[main] Real time: 0.449 sec; CPU: 0.436 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::main_mem] read 24250 sequences (2425000 bp)...
[M::mem_process_seqs] Processed 24250 reads in 36.884 CPU sec, 9.232 real sec
[main] Version: 0.7.10-r960-dirty
[main] CMD: ../bin/bwa-proovread mem -aY -A 5 -B 11 -O 2,1 -E 4,3 -k 8 -W 16 -w 40 -r 1 -D 0 -y 20 -L 30,30 -T 2.5 -t 4 /home/sunyangbo/software/colormap/testData/testCorr/pre_uncorr.fasta /home/sunyangbo/software/colormap/testData/ill.fastq
[main] Real time: 9.397 sec; CPU: 36.976 sec
../runCorr.sh: 行 36: ../bin/samtools: 没有那个文件或目录
../runCorr.sh: 行 36: ../bin/samtools: 没有那个文件或目录
../runCorr.sh: 行 36: ../bin/samtools: 没有那个文件或目录
Could not open file: /home/sunyangbo/software/colormap/testData/testCorr/pre_iter1.sort.sam
rm: 无法删除'/home/sunyangbo/software/colormap/testData/testCorr/pre_iter1.sort.sam': 没有那个文件或目录
[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 314: Success
[E::bwa_idx_load_from_disk] fail to locate the index files
rm: 无法删除'/home/sunyangbo/software/colormap/testData/testCorr/pre_iter1.fasta.amb': 没有那个文件或目录
rm: 无法删除'/home/sunyangbo/software/colormap/testData/testCorr/pre_iter1.fasta.ann': 没有那个文件或目录
rm: 无法删除'/home/sunyangbo/software/colormap/testData/testCorr/pre_iter1.fasta.bwt': 没有那个文件或目录
rm: 无法删除'/home/sunyangbo/software/colormap/testData/testCorr/pre_iter1.fasta.sa': 没有那个文件或目录
../runCorr.sh: 行 44: ../bin/samtools: 没有那个文件或目录
../runCorr.sh: 行 44: ../bin/samtools: 没有那个文件或目录
../runCorr.sh: 行 44: ../bin/samtools: 没有那个文件或目录
Could not open file: /home/sunyangbo/software/colormap/testData/testCorr/pre_iter2.sort.sam
rm: 无法删除'/home/sunyangbo/software/colormap/testData/testCorr/pre_iter2.sort.sam': 没有那个文件或目录

Hello,

Could you please tell me how long does it take to complete a run? I am running ColorMap with 10M PacBio reads and 2512M Illumina reads.

Thanks.

Hi,

Install was a piece of cake (thanks) and I ran the script on my data sets with no troubles!
However, the output was not what I expected. The run returned; .iter1.fasta, .2iter.fasta and _uncorr.fasta.
Are any of these the corrected files?

Cheers.

Hello,
How can we reach the reference genome corresponding to the test data?

realpath command is deprecated and cannot be found on some systems.
In the bash script, try using a different command like readlink for getting the absolute path.